So I tried to figure out, why it worked yesterday and not today. I checked the updates, and the only "critical" update was libtool - from version 2.4.2 to 2.4.2-r1.
Then I installed libtool 2.4.2 and voilà - Alpha Centauri worked flawlessly.

Do you have any idea what's wrong with the updated libtool version? Only thing I could find was the difference in the ABI_X86-Flags.
libtool 2.4.2 is installed with ABI_X86="(-32%) (-64%*) (-x32%)
libtool 2.4.2-r1 is installed with ABI_X86="(64%*) (-32) (-x32)" (I have a 64 bit Gentoo installation).
Could that be the problem? How can i solve it? Do I need some emul-linux-x86 packages (most of them are already installed)?

Thanks!

Update: It seems that libtool 2.4.2-r1 isn't (the only) culprit . Most of the times, it works with the old version of libtool - but not always (which is at least better than with the new version - I couldn't start Alpha Centauri with the -r1 version of libtool once...).